Variant report

Variant	rs6782946
Chromosome Location	chr3:51302865-51302866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10212250	0.82[EUR][1000 genomes]
rs11130282	0.82[EUR][1000 genomes]
rs11712871	0.82[EUR][1000 genomes]
rs12635282	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1383252	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480355	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480357	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480358	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480363	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480365	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1552072	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552073	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904786	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061951	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2355934	0.82[EUR][1000 genomes]
rs2355941	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2355942	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2883811	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34035394	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34251985	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301044	0.82[EUR][1000 genomes]
rs4308313	0.82[EUR][1000 genomes]
rs4340738	0.82[EUR][1000 genomes]
rs4367101	0.82[EUR][1000 genomes]
rs4453876	0.82[EUR][1000 genomes]
rs4528983	0.82[EUR][1000 genomes]
rs4549311	0.82[EUR][1000 genomes]
rs4568176	0.82[EUR][1000 genomes]
rs4568177	0.82[EUR][1000 genomes]
rs4927972	0.82[EUR][1000 genomes]
rs4974093	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4974095	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974097	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974109	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445551	0.82[EUR][1000 genomes]
rs67086923	0.86[ASN][1000 genomes]
rs6763136	0.82[EUR][1000 genomes]
rs6772664	0.82[EUR][1000 genomes]
rs6800805	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6809080	0.82[EUR][1000 genomes]
rs7619584	0.82[EUR][1000 genomes]
rs7628533	0.82[EUR][1000 genomes]
rs7634514	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644957	0.82[EUR][1000 genomes]
rs922612	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9683267	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814041	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9825454	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855442	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855454	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858412	0.82[EUR][1000 genomes]
rs9860962	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9864574	0.82[EUR][1000 genomes]
rs9869123	0.82[EUR][1000 genomes]
rs9878100	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9883739	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6782946	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51252000-51312600	Weak transcription	HSMMtube	muscle
2	chr3:51253400-51312200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:51285400-51308200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:51288200-51319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:51295600-51310800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:51296400-51318800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:51297000-51317400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:51297600-51304000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:51298000-51314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:51298400-51319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:51299400-51307200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:51299400-51307800	Weak transcription	Fetal Brain Female	brain
14	chr3:51299600-51307000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:51299800-51307800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:51301600-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:51302800-51303600	Enhancers	Primary B cells from peripheral blood	blood

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